(a) Overview of prime editing by PE3. After initial
synthesis of the edited strand, 5’ flap excision leaves behind a DNA
heteroduplex containing one edited strand and one non-edited strand. Mismatch
repair resolves the heteroduplex to give either edited or non-edited products.
Nicking the non-edited strand favors repair of that strand, resulting in
preferential generation of duplex DNA containing the desired edit.
(b) The effect of complementary strand nicking on prime editing
efficiency and indel formation. “None” refers to PE2 controls,
which do not nick the complementary strand. (c) Comparison of
editing efficiencies with PE2, PE3, and PE3b (edit-specific complementary strand
nick). Editing efficiencies reflect sequencing reads that contain the intended
edit and do not contain indels among all treated cells, with no sorting. Values
and error bars reflect mean±s.d. of n=3 independent biological
replicates.